4
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2
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1.4k
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 13 months ago by 53k • written 13 months ago by ▴ 60
1
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5
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1.0k
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Package needs internet access
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updated 13 months ago by 68k • written 13 months ago by ▴ 20
1
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2
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543
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Limma Interaction Effect with Covariates
limma DMRcate
13 months ago kitzhu • 0
2
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1
reply
564
views
Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 13 months ago by 68k • written 13 months ago by • 0
1
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2
replies
544
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
1
reply
460
views
eRNAs count
RNASeq DESeq2
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
0
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0
replies
606
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Job: Postdoctoral position in Computational Epigenomics of Aging and Cancer
Aging Epigenetics JobPosting Postdoctor Cancer
13 months ago xiaolong • 0
0
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1
reply
644
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DESeq2 rerun returns different results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
2
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3
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1.4k
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[How to construct a model.matrix ]
limma modelmatrix
updated 13 months ago by 53k • written 14 months ago by • 0
0
votes
1
reply
558
views
Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
0
replies
497
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WGCNA module preservation using only adjacency matrix
WGCNA
14 months ago yang1641 • 0
0
votes
0
replies
286
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
14 months ago Simone • 0
3
votes
4
replies
1.2k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
14 months ago dseauer • 0
0
votes
2
replies
817
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installation error for BiocNeighbors package
BiocNeighbors
14 months ago 育 • 0
0
votes
3
replies
810
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Is it possible to parallelise saveHDF5SummarizedExperiment
HDF5Array
14 months ago • updated 13 months ago Stefano Mangiola ▴ 40
0
votes
1
reply
662
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
votes
2
replies
1.1k
views
Handling biological replicates in DESeq2
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
0
replies
603
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Errors trying to load EPIC v2 data in ChAMP
ChAMP ChAMPdata
14 months ago elgomez • 0
0
votes
1
reply
617
views
forgeBSgenomeDataPkgFromNCBI: Error in find_NCBI_assembly_ftp_dir unable to find FTP dir
BSgenomeForge non-modelorganism unabletofindFTPdir
updated 14 months ago by 16k • written 14 months ago by • 0
0
votes
3
replies
947
views
ChIPpeakAnno can not load data
genomes ChIPpeakAnno
written 16 months ago by • 0
10
votes
7
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2.4k
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Why in Bioconductor community people rarely upvote questions?
bioconductor
updated 14 months ago by 4.2k • written 2.9 years ago by ▴ 50
5
votes
3
replies
29k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 7.0 years ago by ▴ 30
1
vote
3
replies
944
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
0
votes
5
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1.2k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
1
vote
6
replies
1.7k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 14 months ago by 43k • written 14 months ago by ▴ 10
2
votes
4
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2.7k
views
Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 14 months ago by 53k • written 14 months ago by • 0
1
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8
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2.6k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
0
votes
2
replies
590
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 14 months ago by • 0
2
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7
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4.4k
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Annotation for EPICv2
EpicV2 ChAMPdata
updated 14 months ago by • 0 • written 15 months ago by • 0
0
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0
replies
357
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ChIP peaks comparison
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14 months ago user_bioinfo • 0
0
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2
replies
1.0k
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GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
14 months ago GV Yoshikawa • 0
1
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2
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1.5k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
14 months ago Ai • 0
4
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5
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
14 months ago LuciaNhu • 0
0
votes
0
replies
677
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Diffbind: Cut&Run: E-coli spike-in
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14 months ago kim • 0
0
votes
0
replies
416
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
14 months ago brayas13 • 0
2
votes
3
replies
1.3k
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featureCounts segmentation fault with large chromosomes
Rsubread
14 months ago vkkodali ▴ 10
0
votes
1
reply
773
views
Average expression of genes across replicates
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
1
reply
985
views
Spike-in normalization method in ATACseq
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updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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1
reply
934
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single cell RNA seq pseudobulk batch correction
edgeR
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
1
reply
955
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Normalized counts to be used in decoupleR from deseq2 results
decoupleR
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
10
replies
2.9k
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incomplete official symbol mitochondrial genes in org.Hs.eg.db?
org.Hs.eg.db
updated 14 months ago by 68k • written 14 months ago by ★ 4.1k
0
votes
8
replies
1.0k
views
Why are internal functions in the package manual?
roxygen methyLImp2 manual
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
0
replies
347
views
export processed data from flowploidy
flowPloidy
14 months ago Zdenek Skala • 0
0
votes
1
reply
456
views
edit y axis scale in errBarchart?
ddCt
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
2
replies
1.1k
views
Error: 'term_similarity_from_KEGG' not found in simplifyEnrichment package
simplifyEnrichment
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
0
replies
1.5k
views
News: Bioconductor 3.20 is Released!
Bioconductor Release Software
14 months ago shepherl 4.2k
0
votes
0
replies
453
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
14 months ago info ▴ 10
0
votes
1
reply
696
views
probe ID search for SNP (plink)
genomes
updated 14 months ago by 68k • written 14 months ago by • 0
2
votes
2
replies
980
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clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 14 months ago by ★ 1.2k • written 14 months ago by • 0
0
votes
11
replies
2.6k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 9 months ago by • 0 • written 14 months ago by • 0
46,711 results • Page 13 of 935
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Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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